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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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7 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

‘The Cloud is Not Not IT’: Ecological Change in Research Computing in the Cloud

Along with a number of other computing technologies, cloud computing services are increasingly being promoted as a way of enabling openness, reproducibility, and the acceleration of scientific work. While there have been a variety of studies of the cloud in terms of computing performance, there has been little empirical attention to the changes going on around cloud computing at the level of work and practice. Through a qualitative, ethnographic study, we follow a cosmology research group’s transition from a shared high performance computing cluster to a cloud computing service, and examine the cloud service as a coordinative artifact being integrated into a larger ecology of existing practices and artifacts. We find that the transition involves both change and continuity in the group’s coordinative work and maintenance work, and point out some of the effects this adoption has on the group’s larger set of practices. Finally, we discuss practical implications this has for the broader adoption of cloud computing in university-based scientific work.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing

ABSTRACT Targeted amplicon sequencing is widely used in microbial ecology studies. However, sequencing artifacts and amplification biases are of great concern. To identify sources of these artifacts, a systematic analysis was performed using mock communities comprised of 16S rRNA genes from 33 bacterial strains. Our results indicated that while sequencing errors were generally isolated to low-abundance operational taxonomic units, chimeric sequences were a major source of artifacts. Singleton and doubleton sequences were primarily chimeras. Formation of chimeric sequences was significantly correlated with the GC content of the targeted sequences. Low-GC-content mock community members exhibited lower rates of chimeric sequence formation. GC content also had a large impact on sequence recovery. The quantitative capacity was notably limited, with substantial recovery variations and weak correlation between anticipated and observed strain abundances. The mock community strains with higher GC content had higher recovery rates than strains with lower GC content. Amplification bias was also observed due to the differences in primer affinity. A two-step PCR strategy reduced the number of chimeric sequences by half. In addition, comparative analyses based on the mock communities showed that several widely used sequence processing pipelines/methods, including DADA2, Deblur, UCLUST, UNOISE, and UPARSE, had different advantages and disadvantages in artifact removal and rare species detection. These results are important for improving sequencing quality and reliability and developing new algorithms to process targeted amplicon sequences. IMPORTANCE Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Rapid Spaceborne Mapping of Wildfire Retardant Drops for Active Wildfire Management

Aerial application of fire retardant is a critical tool for managing wildland fire spread. Retardant applications are carefully planned to maximize fire line effectiveness, improve firefighter safety, protect high-value resources and assets, and limit environmental impact. However, topography, wind, visibility, and aircraft orientation can lead to differences between planned drop locations and the actual placement of the retardant. Information on the precise placement and areal extent of the dropped retardant can provide wildland fire managers with key information to (1) adaptively manage event resources, (2) assess the effectiveness of retardant slowing or stopping fire spread, (3) document location in relation to ecologically sensitive areas; and perform or validate cost-accounting for drop services. This study uses Sentinel-2 satellite data and commonly used machine learning classifiers to test an automated approach for detecting and mapping retardant application. We show that a multiclass model (retardant, burned, unburned, and cloud artifact classes) outperforms a single-class retardant model and that image differencing (post-application minus pre-application) outperforms single-image models. Compared to the random forest and support vector machine, the gradient boosting model performed the best with an overall accuracy of 0.88 and an F1 Score of 0.76 for fire retardant, though results were comparable for all three models. Our approach maps the full areal extent of the dropped retardant within minutes of image availability, rather than linear representations currently mapped by aerial GPS surveys. The development of this capability allows for the rapid assessment of retardant effectiveness and documentation of placement in relation to sensitive environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow

Subsurface microbial community distribution patterns are influenced by biogeochemical and groundwater fluxes and may inform hydraulic connections along groundwater-flow paths. This study examined the regional-scale microbial community of the Death Valley Regional Flow System and evaluated whether subsurface communities can be used to identify groundwater-flow paths between recharge and discharge areas. Samples were collected from 36 sites in three groundwater basins: Pahute Mesa–Oasis Valley (PMOV), Ash Meadows (AM), and Alkali Flat–Furnace Creek Ranch (AFFCR). Microbial diversity within and between communities varied by location, and communities were separated into two overall groups that affiliated with the AM and PMOV/AFFCR basins. Network analysis revealed patterns between clusters of common microbes that represented groundwaters with similar geochemical conditions and largely corroborated hydraulic connections between recharge and discharge areas. Null model analyses identified deterministic and stochastic ecological processes contributing to microbial community assemblages. Most communities were more different than expected and governed by dispersal limitation, geochemical differences, or undominating processes. However, certain communities from sites located within or near the Nevada National Security Site were more similar than expected and dominated by homogeneous dispersal or selection. Overall, the (dis)similarities between the microbial communities of DVRFS recharge and discharge areas supported previously documented hydraulic connections between: (1) Spring Mountains and Ash Meadows; (2) Frenchman and Yucca Flat and Amargosa Desert; and (3) Amargosa Desert and Death Valley. However, only a portion of the flow path between Pahute Mesa and Oasis Valley could be supported by microbial community analyses, likely due to well-associated artifacts in samples from the two Oasis Valley sites. This study demonstrates the utility of combining microbial data with hydrologic, geologic, and water-chemistry information to comprehensively characterize groundwater systems, highlighting both strengths and limitations of this approach.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Quality control and crop characterization framework for multi-temporal UAV LiDAR data over mechanized agricultural fields

Recent developments in remote sensing are enabling automatic, high resolution, and non-destructive survey of agriculture fields, providing the key basis for advancing plant breeding. Among the used remote sensing modalities, LiDAR has attracted wide attention for its ability to directly provide accurate 3D information. Despite the increasing utilization of LiDAR technology in phenotyping, there is still a lack of effective quality control strategies, in particular, quality control of LiDAR data collected on a multi-temporal basis. This study proposes a targetless framework for multi-temporal LiDAR data quality control and crop characterization in mechanized agricultural fields. Features extracted from the fields – terrain patches and row/alley locations – are utilized for evaluating the vertical and planimetric relative accuracy of the point clouds. Row/alley locations in the field are automatically identified from the point clouds based on the assumption that higher point density and/or higher elevation correspond to plant locations. The performance of the proposed quality control strategies is evaluated using multi-temporal datasets collected in agricultural fields of different sizes, orientation, crops, and growth stages. The result shows that the net vertical and planimetric discrepancies between multi-temporal point clouds are ±3 cm and ±8 cm, respectively. While the former reflects the actual accuracy of the point clouds, the latter is a combined effect of the LiDAR point cloud accuracy, rasterization artifacts, crop type, growth pattern, and wind condition during data acquisition. In terms of row and alley detection, the result shows that the proposed strategy achieves high performance and can deal with different planting orientation, crop types, growth stages, canopy cover, and planting density. In conclusion, this study presents a quality control framework for multi-temporal LiDAR data. Finally, the row and alley detection leads to automated extraction of plots, and hence facilitates the use of remotely sensed data for automated phenotyping.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

New Orthophoto Generation Strategies from UAV and Ground Remote Sensing Platforms for High-Throughput Phenotyping

Remote sensing platforms have become an effective data acquisition tool for digital agriculture. Imaging sensors onboard unmanned aerial vehicles (UAVs) and tractors are providing unprecedented high-geometric-resolution data for several crop phenotyping activities (e.g., canopy cover estimation, plant localization, and flowering date identification). Among potential products, orthophotos play an important role in agricultural management. Traditional orthophoto generation strategies suffer from several artifacts (e.g., double mapping, excessive pixilation, and seamline distortions). The above problems are more pronounced when dealing with mid- to late-season imagery, which is often used for establishing flowering date (e.g., tassel and panicle detection for maize and sorghum crops, respectively). In response to these challenges, this paper introduces new strategies for generating orthophotos that are conducive to the straightforward detection of tassels and panicles. The orthophoto generation strategies are valid for both frame and push-broom imaging systems. The target function of these strategies is striking a balance between the improved visual appearance of tassels/panicles and their geolocation accuracy. The new strategies are based on generating a smooth digital surface model (DSM) that maintains the geolocation quality along the plant rows while reducing double mapping and pixilation artifacts. Moreover, seamline control strategies are applied to avoid having seamline distortions at locations where the tassels and panicles are expected. The quality of generated orthophotos is evaluated through visual inspection as well as quantitative assessment of the degree of similarity between the generated orthophotos and original images. Several experimental results from both UAV and ground platforms show that the proposed strategies do improve the visual quality of derived orthophotos while maintaining the geolocation accuracy at tassel/panicle locations.

54 ENVIRONMENTAL SCIENCES↗